Combined lysis protocol for comprehensive cell lysis

ABSTRACT

Disclosed are methods for lysis of cells, such as bacteria present in microbiomes, that combine three lysis steps—(1) heat, (2) detergent and (3) base—into a single step and that can be completed in a short period of time, e.g., a few minutes. The methods combine a normally incompatible detergent and base lysis, allows for simplified removal of detergent after lysis, and importantly, yields improved quantities of genomic DNA (gDNA) from difficult to lyse bacteria.

CROSS-REFERENCE TO RELATED APPLICATION

This application is a continuation of, and claims priority to, U.S.patent application Ser. No. 15/854,157, filed Dec. 26, 2017, whichclaims priority to U.S. provisional patent application No. 62/440,171,filed Dec. 29, 2016, the contents of each of which are incorporatedherein by reference in their entireties.

FIELD OF THE DISCLOSURE

Disclosed are methods for lysing cells to release or extract genomic DNA(gDNA) from inside of the cells. The disclosed methods combine heat,detergent and base in a single tube and can be completed in a fewminutes. The methods combine a normally incompatible detergent and basethat facilitate post-lysis removal of detergent without extra steps, andthe combination creates unexpected synergies lacking in sequentialtreatment protocols, that greatly reduces the number of steps andhands-on time, while yielding improved representation of gDNA, forexample, from difficult to lyse bacteria in microbiome samples.

BACKGROUND OF THE DISCLOSURE

Many cell-based and DNA-based analytical methods require releasing DNAfrom inside the cell to facilitate analysis. Opening the cells torelease the DNA is called lysis.’ For example, methods used toinvestigate the microbiome using DNA sequencing techniques first requirelysis of microbes so the DNA can be extracted. Most microbiomes arecommunities of bacteria, archaea and fungi that vary tremendously intheir susceptibility to lysis techniques. Differential susceptibilitypresents a significant problem to researchers, who want to ensure thatthe toughest (usually Gram-positive) and the easiest (usuallyGram-negative) to lyse bacteria are represented in proportion to theirpopulation in the original sample. Unfortunately, most microbial lysisprotocols work well for some microbes, but poorly for others.Additionally, rapid and simple alkaline lysis techniques used to recoverplasmid DNA typically also remove the microbial genomic DNA, which isthe target for microbiome screening (Alkaline Lysis opens cells butremoves gDNA—Birnboim, H. C. and Doly, A rapid alkaline extractionprocedure for screening recombinant plasmid DNA, Nucleic Acids Res.7(6), 1979, 1513-1524; KOH lysis recovers bacterial genomicDNA-Raghunathan, Arumugham et al. “Genomic DNA Amplification from aSingle Bacterium.” Applied and Environmental Microbiology 71.6 (2005):3342-3347. PMC. Web. 29 Sep. 2016). There are multiple lysis techniquesknown in the art that attack cellular integrity based on differentbiochemical methods, including lysozyme (enzymatic attack on thepeptidoglycan cell wall), strong base (chemical attack), detergent(solubilizes cell membranes), bead beating or shaking (mechanicaldisruption), and heat (Comparison of lysis techniques formicrobiome-Sanqing Yuan, Dora B. Cohen, Jacques Ravel, Zaid Abdo, LarryJ. Forney. Evaluation of Methods for the Extraction and Purification ofDNA from the Human Microbiome. PLoS ONE 7(3): e33865. doi:10.1371/journal.pone.0033865; DNA extraction methods affect microbiomeprofiling results: Wagner Mackenzie B, Waite D W, Taylor M W. Evaluatingvariation in human gut microbiota profiles due to DNA extraction methodand inter-subject differences. Frontiers in Microbiology. 2015; 6: 130.doi:10.3389finicb.2015.00130). Most published or commercially availableDNA preparation methods use one or more of these methods to lyse cells,usually in sequential steps that can take a significant amount of time,especially when handling many samples at once. While individual lysismethods are usually sufficient for applications where incomplete orpartial lysis yields sufficient DNA for the protocol being performed,they often do not yield DNA from microbiome samples in proportion to theoriginal community, and may fail to lyse certain microbes altogether.For example, a detergent-based lysis may disrupt a subset of cells withweak cell walls and strong cell membranes, but not opendetergent-resistant microbes with strong cell walls, leading tounder-representation or absence of DNA from detergent resistant cells inthe resulting DNA preparation. In another example, bead beating ofmicrobes sufficient to lyse cells with strong cell membranes may shearor destroy DNA released early in the process from easily lysed cells.Additionally, the various methods of lysis tend to be incompatible witheach other, and need to be performed sequentially if used incombination. For example, lysozyme will not work in the presence ofdetergents or strong base. Certain detergents precipitate in thepresence of strong base. Bead beating is difficult to combine with aheating process. While individual shortcomings may be overcome byrunning separate lysis protocols in series, this increases thecomplexity, time, and cost involved. Importantly, detergents such assodium dodecyl sulfate (SDS) must be removed after lysis, because SDSinterferes with downstream DNA manipulation. Additionally, certainmicrobes may be resistant to lysis protocols run sequentially, dependingon protocol order. For example, certain microbes with toughpeptidoglycan cell walls may have an outer envelope of lipid bi-layerthat protects from an initial treatment with strong base or lysozyme.Only a simultaneous combination of multiple methods may be effective, ora long sequence of multiple steps, to yield DNA from all microbes in asample.

The methods disclosed herein streamline lysis for applications andtechniques where proportional lysis is desired or necessary, such asmicrobiome research, by combining multiple lysis methods into a simple,rapid protocol that yields a more representative DNA profile across asample containing different cellular constituents, such as themicrobiome.

BRIEF SUMMARY

Disclosed are methods for lysis of cells, such as bacteria present inmicrobiomes, that combine three lysis steps—(1) heat, (2) detergent and(3) base—into a single step and that can be completed in a short periodof time, e.g., a few minutes. The methods combine a normallyincompatible detergent and base lysis, allows for simplified removal ofdetergent after lysis, and importantly, yields improved quantities ofgenomic DNA (gDNA) from difficult to lyse bacteria.

Disclosed herein is a method for lysing cells in a sample to release DNAfrom the cells, comprising: (a) mixing an aqueous solution containingbiologic cells with (i) an ionic detergent and (ii) a base capable ofprecipitating the ionic detergent; (b) heating the aqueous solution toat least 50° C. for a time effective to dissolve the ionic detergent;(c) cooling the aqueous solution to 40° C. or less for a time effectiveto precipitate the ionic detergent; and (d) separating the precipitatefrom the aqueous solution, wherein DNA released from the biologic cellsis present in the aqueous solution after separation of the precipitate.

In some embodiments, the ionic detergent is selected from the groupconsisting of: sodium dodecyl sulfate (SDS), N-Lauroylsarcosine sodiumsalt, or sodium deoxycholate. In some embodiments, the concentration ofthe ionic detergent is from about 0.1% to about 10%. In someembodiments, the ionic detergent is sodium dodecyl sulfate (SDS) at aconcentration of about 1%.

In some embodiments, the base is selected from the group consisting of:potassium hydroxide (KOH), lithium hydroxide (LiOH), sodium hydroxide(NaOH), rubidium hydroxide (RbOH), cesium hydroxide (CsOH), calciumhydroxide (Ca(OH)₂), strontium hydroxide (Sr(OH)₂), and barium hydroxide(Ba(OH)₂). In some embodiments, the concentration of the base is fromabout 0.05 molar to about 1 molar. In some embodiments, the base ispotassium hydroxide (KOH) at a concentration of about 0.2 molar.

In some embodiments, the detergent is combined with a base thatprecipitates the detergent at low temperature, but permits the detergentto dissolve at high temperature.

In some embodiments, the ionic detergent is sodium dodecyl sulfate (SDS)at a concentration of 1% by weight and the base is and aqueous solutioncontaining potassium hydroxide (KOH) at a concentration of 0.2 molar.

In some embodiments, the heating is conducted at a temperature range offrom about 50° C. to about 100° C. In some embodiments, the heating isconducted at a temperature of about 65° C. In some embodiments, theheating is conducted at a temperature of about 95° C. In someembodiments, the heating is conducted for at least 1 minute.

In some embodiments, the cooling is conducted at a temperature range offrom about 4° C. to about 40° C. In some embodiments, the cooling isconducted at a temperature of about 20° C. to about 25° C. In someembodiments, the cooling is conducted for at least 30 seconds.

In some embodiments, the separating is conducted by a method selectedfrom the group consisting of: centrifugation, filtration, gravitysettling.

In some embodiments, the biologic cells originate from a sample selectedfrom the group consisting of: feces, cell lysate, tissue, blood, tumor,tongue, tooth, buccal swab, phlegm, mucous, wound swab, skin swab,vaginal swab, or any other biological material or biological fluidoriginally obtained from a human, animal, plant, or environmentalsample, including raw samples, complex samples, mixtures, and microbiomesamples.

In some embodiments, the biologic cells originate from an organismselected from the group consisting of: multicellular organisms,unicellular organisms, prokaryotes, eukaryotes, microbes, bacteria,archaea, protozoa, algae and fungi.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1a shows the white SDS precipitate in the potassium hydroxide(KOH+SDS) tube (right), at room temperature. The tube at left shows 1%SDS in the absence of KOH as a clear solution.

FIG. 1b shows the white SDS precipitate in the potassium hydroxide(KOH+SDS) tube (left), at room temperature. The tube at right shows 1%SDS in the presence of NaOH as a clear solution, demonstrating that NaOHdoes not precipitate SDS.

FIG. 2 depicts PCR barcoding results of 16S rRNA genes for 8 microbiomesamples. The 1500 base amplicon in each of the 8 lanes is tagged with adifferent DNA barcode.

FIG. 3 is a graph showing a comparison of average microbial abundancesat phylum level in multiple samples lysed using sequential lysis stepsof detergent and bead beating or the combined lysis method describedherein. There is a higher abundance of the more difficult to lyseFirmicutes using the Shoreline Biome method.

FIG. 4 is a graph showing a comparison of average microbial abundancesat genus level in multiple samples lysed using sequential lysis steps ofdetergent and bead beating or the combined lysis method describedherein. This demonstrates that the phylum level abundances in FIG. 3correspond to the appearance of an increased quantity and diversity ofFirmicutes at the genus level.

DETAILED DESCRIPTION

The subject matter that is regarded as the invention is particularlypointed out and distinctly claimed in the claims at the conclusion ofthe specification. The foregoing and other objects, features, andadvantages of the invention will be apparent from the following detaileddescription taken in conjunction with the accompanying drawings.

DNA located inside cells, such as bacteria and archaea in a microbiome,can be released by lysing the cells. To investigate a microbiome, cellsin the target microbiome are lysed, after which the resulting DNA inthis description can either be sequenced directly (‘shotgun’ sequencing,not shown), or used as template in PCR amplification targeting a geneticregion such as the 16S rRNA gene, present in all bacteria and archaea.The 16S gene is used as an example herein because it can be used as a‘fingerprint’ identification method for microbes, requiring ˜1000× lesssequencing than the shotgun method. Microbes can be identified usingtheir 16S rRNA gene sequence, which varies slightly in most, if not all,bacteria and archaea. The variation in 16S gene sequence means thatindividual species of bacteria and archaea have characteristic DNAvariations (‘fingerprints’) in the 16S rRNA gene that serve asidentifiers for those species or strains. Kits, protocols and softwareenable comprehensive fingerprinting of the microbes in a sample, andpermits simultaneous 16S rRNA fingerprinting of many samples at once, athigh resolution, using the full length 16S rRNA gene (see, for example,U.S. Provisional Patent Application No. 62/266,072 titled “Methods forDNA Preparation for Multiplex High Throughput Targeted Screening” byMark Driscoll and Thomas Jarvie, that is incorporated herein byreference in its entirety). Known microbes can be identified aftersequencing by mapping the DNA sequence of the 16S gene to a database ofknown reads. Unknown microbes will contain 16S DNA sequences that aredifferent from any of the microbes in the database, but can be trackedusing their unique 16S sequence. In addition, the number of readsobtained for each microbe in a sample can reveal the relative abundancesof each microbe in a sample. The relative abundance of specific microbescan be an important indicator of the state of each individualmicrobiome. Lysis techniques that change relative abundances ofmicrobes, or leave out DNA from certain microbes altogether, can lead tosequencing results that incorrectly characterize the state of themicrobiomes being studied. The methods described herein can be used toachieve the correct relative abundances of microbes from a sample.

The lysis process can be used for ‘shotgun’ microbiome sequencing aswell, where the DNA is subjected to sequencing after lysis without 16SrRNA gene amplification. The shotgun method is used when investigatorswant to read all DNA sequences in a sample, not just the 16S gene frombacteria and archaea. For example, high depth shotgun microbiome DNAsequencing may reveal the full DNA genomic sequence from unknownbacteria/archaea, as well as fungi, or multicellular eukaryotes, viralDNA, or any other DNA containing organisms. Since a full bacterialgenome can be millions of bases long (thousands of times larger than the16S gene), fungal genomes can be more than a hundred million bases, andeukaryotic genomes can be billions of bases long, a shotgun microbiomeprofile can require thousands of times more sequencing than a 16S rRNAgene microbiome profile, with correspondingly greater time and costs.Although only the 16S profiling method is discussed in this example, thelysis protocol described herein provides the same advantages to bothshotgun and 16S rRNA microbiome sequencing approaches.

The following is an example of the disclosed methods for the 16S rRNAgene microbiome sequencing approach:

Step 1. A microbiome sample was dispersed into an aqueous solutioncontaining 2% by weight of sodium dodecyl sulfate (SDS).

Step 2. 0.4M KOH was added and SDS detergent precipitated as whiteflocculent. In this example, the detergent (1% SDS) is precipitated bythe base (0.2M KOH).

Step 3. The tube was capped and heated (temperature can range from about50° C. to about 100° C.). SDS dissolves at temperatures above 50° C.Heat and KOH attack the peptidogycan cell wall, and SDS solubilizesmembranes that protect microorganisms from the damaging effects of theKOH and heat. This combination of steps is synergistic, becausesequential exposure to KOH, SDS, and heat, in contrast to the combinedexposure described here, may not yield the same results because of theway that microbial cell walls and membranes are structured. Heatactually allows SDS to work in the presence of strong base, resulting ina unique simultaneous combination of three different lysis techniques.

Step 4. After heating, the sample was brought back to room temperature(e.g., below 40° C.) to precipitate the SDS detergent.

Step 5. The sample was centrifuged briefly to pelletize the SDSdetergent (no additions necessary, rapid removal of detergent).

Step 6. The supernatant was moved to tube containing 500 mM Tris bufferor equivalent, pH 8.5. The released DNA is now ready for analysis by 16SrRNA PCR (as described below), or can be stored or purified further forother uses.

Each DNA sample was subjected to PCR amplification a method whichassigns unique DNA barcodes to each sample. An example PCR reaction for8 different microbiomes is shown in FIG. 2 where human fecal samples 1-8were lysed according to the protocol described above in Steps 1-6, or bya standard protocol with sequential detergent/bead beating steps. Eachsample was PCR amplified using primers to the 1500 bp 16S rRNA gene,with a different DNA barcode for each sample. Samples were pooled forDNA sequencing after PCR. Since the reads from each sample contained aunique identifying DNA barcode, they can be sorted by sample aftersequencing. Reads output by the sequencer are sorted by sample usingbarcodes and mapped to a database to identify known microbes, unknownmicrobes, and their relative proportion in each sample.

After sorting by barcode into sample of origin, identification by genus,and quantitation of the number of reads for each genus by softwareanalysis of the reads, the reads for each microbiome were compared.Depending on the experimental design, there are a number of ways theoutput could be compared. In FIG. 3, the quantity of each microbe in amicrobiome is included in a 100% stacked bar plot for two samples. Thismethod allows for simple, direct comparison of microbiomes. Other usefulcomparisons include phylum level differences, species or strain leveldifferences, or other taxonomic levels.

For multiple samples, a standard method using sequential lysis steps ofdetergent and bead beating was compared to the combined lysis methoddescribed herein. As shown in FIG. 3, Gram-positive Firmicutes increasedin abundance from ˜30% to over 60% of the microbiome. Firmicutes areGram positive bacteria with strong cell walls that tend to be difficultto lyse. This demonstrates that the lysis method described herein isbetter at lysing microbes with strong cell walls. Easy to lyseBacteriodetes and Verrucomicrobia phyla decreased proportionally, aswould be expected when using a 100% stacked bar plot.

FIG. 4 depicts average abundances at the genus level for the samesamples shown in FIG. 3. FIG. 4 is a higher-resolution view of theFirmicutes that are under-represented using the standard method usingsequential lysis steps of detergent and bead beating. The bar plot ofgenus level differences in abundance show that there are five Firmicutesgenuses under-represented using the standard sequential lysis method(Listeria, Blautia, Lachnospiracea Incertae Sedis, Butyrococcus,Ruminococcus), and the relative representation of the Bacteroides andAkkermansia is artificially high using the standard method. Thisparallels the phylum level differences in FIG. 3, while showing thatindividual Firmicutes genus levels can be significantlyunder-represented using the standard method.

One or more embodiments of the present invention have been described.Nevertheless, it will be understood that various modifications may bemade without departing from the spirit and scope of the invention.Accordingly, other embodiments are within the scope of the followingclaims.

1.-17. (canceled)
 18. A method for releasing genomic DNA from biologiccells in a sample by lysing the cells, comprising the sequential stepsof: a) producing a mixture solution by mixing an aqueous solutioncontaining the biologic cells from the sample with (i) an amount of anionic detergent, and (ii) an amount of a base such that the ionicdetergent and the base in the mixture solution are at concentrationseffective for releasing the genomic DNA from the cells by lysing thecells after the ionic detergent is dissolved in the mixture solution; b)heating the mixture solution to at least about 50° C. for a time suchthat the ionic detergent is dissolved in the mixture; c) cooling themixture solution to 40° C. or less for a time effective to precipitatethe ionic detergent, thereby producing a precipitate comprising theionic detergent; and d) separating the precipitate comprising the ionicdetergent from the mixture solution, wherein the genomic DNA releasedfrom the biologic cells is present in a solution generated by saidseparating the precipitate comprising the ionic detergent from themixture solution; and wherein the genomic DNA released from the biologiccells is ready for analysis, PCR amplification, sequencing,purification, or storage.
 19. The method of claim 18, wherein the ionicdetergent is selected from the group consisting of: sodium dodecylsulfate (SDS), N-Lauroylsarcosine sodium salt, and sodium deoxycholate.20. The method of claim 18, wherein the ionic detergent of the mixturesolution in step b) is from about 0.1% by weight to about 10% by weight.21. The method of claim 18, wherein the ionic detergent of the mixturesolution in step b) is about 1% by weight.
 22. The method of claim 18,wherein the base is selected form the group consisting of: potassiumhydroxide (KOH), lithium hydroxide (LiOH), sodium hydroxide (NaOH),rubidium hydroxide (RbOH), cesium hydroxide (CsOH), calcium hydroxide(Ca(OH)₂), strontium hydroxide (SR(OH)₂), and barium hydroxide(Ba(OH)₂).
 23. The method of claim 18, wherein the base of the mixturesolution in step b) is from about 0.05 molar to about 1 molar.
 24. Themethod of claim 18, wherein the base of the mixture solution in step b)is about 0.2 molar.
 25. The method of claim 18, wherein the ionicdetergent of the mixture solution in step b) is 1% by weight and thebase of the mixture solution in step b) is 0.2 molar.
 26. The method ofclaim 18, wherein the at least about 50° C. is a temperature range fromat least about 50° C. to about 100° C.
 27. The method of claim 26,wherein the heating step is conducted at a temperature about 95° C. 28.The method of claim 27, wherein the time conducted in the heating stepis at least 0.25 minutes.
 29. The method of claim 18, wherein the 40° C.or less is at a temperature range from about 4° C. to 40° C.
 30. Themethod of claim 29, wherein the cooling temperature range from about 4°C. to 40° C. is about 20° C. to about 25° C.
 31. The method of claim 30,wherein the time conducted in the cooling step is for at least 0.25minutes.
 32. The method of claim 18, wherein the separating step isconducted by a method selected from the group consisting of:centrifugation of the mixture solution, filtration of the mixturesolution and gravity settling of the mixture solution.
 33. The method ofclaim 18, wherein the sample is selected from the group consisting of:feces, cell lysate, tissue, blood, tumor, tongue, tooth, buccal swab,phlegm, mucous, wound swab, skin swab, vaginal swab, or any otherbiological material or biological fluid originally obtained from ahuman, animal, plant, or environmental samples, raw samples, complexsamples, mixtures of samples, and microbiome samples.
 34. The method ofclaim 18, wherein the sample is from an organism selected from the groupconsisting of: multicellular organisms, unicellular organisms,prokaryotes, eukaryotes, microbes, bacteria, archaea, protozoa, algae,fungi and viruses.
 35. The method of claim 18, wherein the DNA releasedfrom the biologic cells is in relative abundance with, or has thecorrect relative abundance compared to, the relative abundance of thebiologic cells in the sample.
 36. The method of claim 18, wherein theDNA released from the biologic cells is proportional to, or inproportion with, the biological cells in the sample.